Exon is an execution engine designed to work with bioinformatics data. It features:

• SQL based access to bioinformatics data -- general DML and some DDL support
• Support for many file formats from bioinformatics, proteomics, and others
• Local filesystem and object storage support
• Arrow FFI primitives for multi-language support

Installation

Exon is available via crates.io. To install, run:

cargo add exon

Documentation

• Rust documentation is available here.
• General documentation is available here.

Related Projects

• Exon R Bindings
• BioBear

Benchmarks

Please see the benchmarks README for more information.

lib.rs:

Exon is a library to facilitate open-ended analysis of scientific data, ease the application of ML models, and provide a common data interface for science and engineering teams.

Overview

The main interface for users is through datafusion's SessionContext plus the ExonSessionExt extension trait. This has a number of convenience methods for loading data from various sources.

See the read_* methods on ExonSessionExt for more information. For example, read_fasta, or read_gff. There's also a read_inferred_exon_table method that will attempt to infer the data type and compression from the file extension for ease of use.

To facilitate those methods, Exon implements a number of traits for DataFusion that serve as a good base for scientific data work. See the datasources module for more information.